Gene discovery in grapes: the grape genome project
Ablett, EM, Lee, LS, Pacey-Miller, T, Waters, DLE, Miao, GH, Dolan, M, Hanafey, M, Tingey, SV & Henry, RJ 2003, 'Gene discovery in grapes: the grape genome project', paper presented to the Congress on In Vitro Biology, Oregon, USA, 30 May - 4 June.
The grape genome project is combining large-scale EST analysis, a 16 times BAC library, and functional analysis of grape genes in Arabidopsis to advance gene discovery in Vitis vinifera. From two projects undertaken by Southern Cross University, 44,928 grape (Vitis vinifera) ESTs have been produced from a range of tissues and cultivars, and these code for approximately 18,500 grape genes. With the grape genome having a size of 511 Mb, similar to rice, we estimate that the 18,500 genes represent 2/3 of the grape genome. The first project produced almost 5,000 sequences (2,330 distinct gene matches). The list of genes is being made available via the World Wide Web and includes transcripts relating to proteins involved in the whole range of functional categories. The Webbased catalogue of the gene functions revealed from the first project and the method of access to selected gene sequences may be viewed at http://wwwdev.scu.edu.au/research/cpcg/genomics/. ESTO˜ s from both projects have been used in ‘‘electronic northern’’ and microarray analysis to investigate new aspects of gene function from expression data. The abundance of transcripts with predicted cellular roles in leaf, berry and developing buds, were estimated by classifying the EST primary BLAST matches into 80 functional categories. Comparison with ‘‘electronic northern’’ analysis of 33 human tissues suggests plant cells may involve their cellular machinery to a greater extent in specialised activities than is the case in animal cells. Hybridization of mRNA sampled during budburst to arrayed ESTO˜ s indicate altered levels of expression of large numbers of genes before and during budburst, and profiles of candidate genes with possible roles in this process have been analysed.